I haven't tried much gardening on Pets yet so my only thought on this is that maybe the seed is placed to close to another object, be it another plant or a wall/fence etc, I often got that problem on the sims 3. Try placing the seed from storage/inventory in build mode in an open space (atleast 1 large grid square away from other objects), go back to live mode and see if you can plant it, if you manage to plant it you should be able to move the plant in build mode should you wish to do so.
If all else fails you could try moving house and then try planting the onion/seed just to see if the lot was bugged or something. Moving seems to fix quite a few bugs for the console versions providing it is a bug of course.